Hello,
For an analysis, I am using the KapCophen pipeline (https://github.com/miwipe/KapCopenhagen). I merged 26 different BAM files using “samtools merge” and obtained a sam.gz file. To sort the read names of this file, I used the gz-sort tool mentioned in the “sorting alignments” section of the pipeline above. Afterwards, when I tried to analyze the sam.gz file using the “metaDMG-cpp lca” command, I received the following error:
-> Will output the reads that has lca below family : '$home '
-> ERROR: We require files to be sorted by readname, will exit
Input alignment file is not sorted.merging bam files of $sample
I carefully inspected the sorted file in detail, and it looks properly sorted. So I was wondering whether a similar issue has been encountered before.
Best wishes,
Sevgi
Hello,
For an analysis, I am using the KapCophen pipeline (https://github.com/miwipe/KapCopenhagen). I merged 26 different BAM files using “samtools merge” and obtained a sam.gz file. To sort the read names of this file, I used the gz-sort tool mentioned in the “sorting alignments” section of the pipeline above. Afterwards, when I tried to analyze the sam.gz file using the “metaDMG-cpp lca” command, I received the following error:
-> Will output the reads that has lca below family : '$home '
-> ERROR: We require files to be sorted by readname, will exit
Input alignment file is not sorted.merging bam files of $sample
I carefully inspected the sorted file in detail, and it looks properly sorted. So I was wondering whether a similar issue has been encountered before.
Best wishes,
Sevgi